.. Doppio Tomography Tutorial documentation master file, created by
   sphinx-quickstart on Tue Feb 18 13:09:38 2025.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

.. _installation:


Software Installation
==================================

Tomography pipeline in Doppio is built on top of several software packages.
To get the most of the pipeline you need following software packages installed on your PATH

Relion 5.0
---------------------------------
Relion 5.0 Installation is covered `<https://relion.readthedocs.io/en/latest/Installation.html>`_.

IMOD
---------------------------------
IMOD Installation is covered `<https://bio3d.colorado.edu/imod/doc/guide.html>`_.

These are some quick steps to install IMOD on Ubuntu 20.04 into the default location in the system.

.. code-block:: bash

    wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_5.1.1_RHEL8-64_CUDA12.0.sh
    sh imod_5.1.1_RHEL8_CUDA12.0.sh

The above script will install Imod in /usr/local and copy /usr/local/IMOD/IMOD-linux.sh to /etc/profile.d, which will be called on startup to import appropriate paths (i.e. IMOD_DIR).
For whatever reason, if the above script fails to load IMOD, you can set variables as below:

.. code-block:: bash
   
    export IMOD_DIR='/usr/local/IMOD'
    export PATH="/usr/local/IMOD/bin:$PATH"
    export LD_LIBRARY_PATH="/usr/local/IMOD/lib:$LD_LIBRARY_PATH"



AreTomo2
---------------------------------
AreTomo2 Installation is in `<https://github.com/czimaginginstitute/AreTomo2#installation>`_.


CTFFind4.1
---------------------------------
CTFFind4 can be downloaded from `<https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt>`_.
To install, unpack the tarball and add the path to the binary to your PATH.

.. code-block:: bash
   
    tar -xvf ctffind4.1.14-linux64.tar.gz 
    export PATH="/path/to/ctffind:$PATH"



MotionCor2
---------------------------------
RELION has its own implementation of MotionCor2 for CPUs. We recommend using it because that allows to take the full advantage of the Bayesian polishing.
However, if you want to use the GPU version of MotionCor2, you can download it from `<https://emcore.ucsf.edu/ucsf-software>`_.  
To install. unpack the zip file and add the path to the binary to your PATH.

.. code-block:: bash
    
    mkdir -p ~/MotionCor2
    cd ~/MotionCor2
    mv ~/Downloads/MotionCor2_1.6.4_Mar31_2023.zip .
    unzip MotionCor2_1.6.4_Mar31_2023.zip
    ln -s MotionCor2_1.6.4_Cuda121_Mar312023 MotionCor2
    export PATH="${HOME}/MotionCor2:$PATH"



CryoCARE
---------------------------------
cryoCARE Installation is covered `<https://pypi.org/project/cryoCARE/>`_.